[2024-01-24 13:32:34,998] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:35,001] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:35,001] [INFO] DQC Reference Directory: /var/lib/cwl/stg78f6408a-5a55-4929-8c50-56e97f4296af/dqc_reference
[2024-01-24 13:32:36,395] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:36,400] [INFO] Task started: Prodigal
[2024-01-24 13:32:36,400] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc012e36-d390-4f32-8487-7374f27d8783/GCF_009689005.1_ASM968900v1_genomic.fna.gz | prodigal -d GCF_009689005.1_ASM968900v1_genomic.fna/cds.fna -a GCF_009689005.1_ASM968900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:00,537] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:00,537] [INFO] Task started: HMMsearch
[2024-01-24 13:33:00,537] [INFO] Running command: hmmsearch --tblout GCF_009689005.1_ASM968900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78f6408a-5a55-4929-8c50-56e97f4296af/dqc_reference/reference_markers.hmm GCF_009689005.1_ASM968900v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:01,030] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:01,031] [INFO] Found 6/6 markers.
[2024-01-24 13:33:01,093] [INFO] Query marker FASTA was written to GCF_009689005.1_ASM968900v1_genomic.fna/markers.fasta
[2024-01-24 13:33:01,094] [INFO] Task started: Blastn
[2024-01-24 13:33:01,094] [INFO] Running command: blastn -query GCF_009689005.1_ASM968900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78f6408a-5a55-4929-8c50-56e97f4296af/dqc_reference/reference_markers.fasta -out GCF_009689005.1_ASM968900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:01,809] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:01,817] [INFO] Selected 14 target genomes.
[2024-01-24 13:33:01,817] [INFO] Target genome list was writen to GCF_009689005.1_ASM968900v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:01,831] [INFO] Task started: fastANI
[2024-01-24 13:33:01,831] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc012e36-d390-4f32-8487-7374f27d8783/GCF_009689005.1_ASM968900v1_genomic.fna.gz --refList GCF_009689005.1_ASM968900v1_genomic.fna/target_genomes.txt --output GCF_009689005.1_ASM968900v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:24,632] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:24,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78f6408a-5a55-4929-8c50-56e97f4296af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:24,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78f6408a-5a55-4929-8c50-56e97f4296af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:24,647] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:33:24,647] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:24,647] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Desulfosarcina ovata subsp. ovata	strain=oXyS1	GCA_009689005.1	2752305	83564	type	True	100.0	2532	2543	95	conclusive
Desulfosarcina ovata subsp. sediminis	strain=28bB2T	GCA_009688985.1	885957	83564	type	True	97.0245	1967	2543	95	conclusive
Desulfosarcina cetonica	strain=JCM 12296	GCA_001311845.1	90730	90730	type	True	81.1778	992	2543	95	below_threshold
Desulfosarcina alkanivorans	strain=PL12	GCA_009688945.1	571177	571177	type	True	79.3328	707	2543	95	below_threshold
Desulfosarcina widdelii	strain=PP31	GCA_009688965.1	947919	947919	type	True	79.0721	642	2543	95	below_threshold
Desulfotignum phosphitoxidans	strain=DSM 13687	GCA_000350545.1	190898	190898	type	True	76.4977	95	2543	95	below_threshold
Desulfonema magnum	strain=4be13	GCA_017377395.1	45655	45655	type	True	76.2445	57	2543	95	below_threshold
Desulfotignum balticum	strain=DSM 7044	GCA_000421285.1	115781	115781	type	True	76.1998	95	2543	95	below_threshold
Desulfospira joergensenii	strain=DSM 10085	GCA_000420085.1	53329	53329	type	True	75.8635	84	2543	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	74.8044	51	2543	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:24,650] [INFO] DFAST Taxonomy check result was written to GCF_009689005.1_ASM968900v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:24,651] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:24,651] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:24,651] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78f6408a-5a55-4929-8c50-56e97f4296af/dqc_reference/checkm_data
[2024-01-24 13:33:24,653] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:24,727] [INFO] Task started: CheckM
[2024-01-24 13:33:24,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009689005.1_ASM968900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009689005.1_ASM968900v1_genomic.fna/checkm_input GCF_009689005.1_ASM968900v1_genomic.fna/checkm_result
[2024-01-24 13:34:33,423] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:33,424] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:33,453] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:33,453] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:33,453] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009689005.1_ASM968900v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:33,454] [INFO] Task started: Blastn
[2024-01-24 13:34:33,454] [INFO] Running command: blastn -query GCF_009689005.1_ASM968900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78f6408a-5a55-4929-8c50-56e97f4296af/dqc_reference/reference_markers_gtdb.fasta -out GCF_009689005.1_ASM968900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:34,512] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:34,518] [INFO] Selected 14 target genomes.
[2024-01-24 13:34:34,518] [INFO] Target genome list was writen to GCF_009689005.1_ASM968900v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:34,600] [INFO] Task started: fastANI
[2024-01-24 13:34:34,601] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc012e36-d390-4f32-8487-7374f27d8783/GCF_009689005.1_ASM968900v1_genomic.fna.gz --refList GCF_009689005.1_ASM968900v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009689005.1_ASM968900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:51,011] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:51,027] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:51,028] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_009689005.1	s__Desulfosarcina ovata	100.0	2533	2543	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	97.03	97.03	0.77	0.77	2	conclusive
GCF_001311845.1	s__Desulfosarcina cetonica	81.1937	985	2543	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	99.91	99.91	0.98	0.98	2	-
GCF_009688945.1	s__Desulfosarcina alkanivorans	79.3668	702	2543	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009688965.1	s__Desulfosarcina widdelii	79.0397	641	2543	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014237405.1	s__Desulfosarcina sp014237405	78.5223	514	2543	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	99.69	99.69	0.89	0.89	3	-
GCA_018224455.1	s__Desulfosarcina sp018224455	78.3481	413	2543	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352605.1	s__Desulfosarcina sp002352605	78.2958	343	2543	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002747175.1	s__Desulfosarcina sp002747175	77.2988	154	2543	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	97.81	97.81	0.57	0.57	2	-
GCA_011390985.1	s__JAABRJ01 sp011390985	76.9065	111	2543	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__JAABRJ01;g__JAABRJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003715.1	s__JABDIN01 sp013003715	76.4988	91	2543	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__JABDIN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018399285.1	s__Desulfotignum sp018399285	76.4722	68	2543	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421285.1	s__Desulfotignum balticum	76.182	96	2543	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	96.875	N/A	N/A	N/A	N/A	1	-
GCF_000420085.1	s__Desulfospira joergensenii	75.8791	83	2543	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903953895.1	s__RAAP-1 sp903953895	75.7849	59	2543	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfatirhabdiaceae;g__RAAP-1	95.0	99.36	98.92	0.95	0.91	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:51,029] [INFO] GTDB search result was written to GCF_009689005.1_ASM968900v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:51,030] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:51,033] [INFO] DFAST_QC result json was written to GCF_009689005.1_ASM968900v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:51,033] [INFO] DFAST_QC completed!
[2024-01-24 13:34:51,033] [INFO] Total running time: 0h2m16s